264,963 results match your criteria Bioinformatics and Biology Insights [Journal]


Detecting moderate or complex congenital heart defects in adults from an electronic health records system.

J Am Med Inform Assoc 2018 Dec;25(12):1634-1642

Emory University School of Medicine, Atlanta, GA, USA.

Background: The prevalence of moderate or complex (moderate-complex) congenital heart defects (CHDs) among adults is increasing due to improved survival, but many patients experience lapses in specialty care or their CHDs are undocumented in the medical system. There is, to date, no efficient approach to identify this population.

Objective: To develop and assess the performance of a risk score to identify adults aged 20-60 years with undocumented specific moderate-complex CHDs from electronic health records (EHR). Read More

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December 2018
3 Reads

Role of electronic patient reported safety incidents in improving patient safety and care.

Int J Qual Health Care 2018 Dec 12. Epub 2018 Dec 12.

Graduate Institute of Bioinformatics, Taipei Medical University, Taipei, Taiwan.

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December 2018

CNValidator: validating somatic copy-number inference.

Bioinformatics 2018 Dec 12. Epub 2018 Dec 12.

Department of Genome Sciences, University of Washington, Seattle, WA, USA.

Motivation: CNValidator assesses the quality of somatic copy number calls based on coherency of haplotypes across multiple samples from the same individual. It is applicable to any copy number calling algorithm which makes calls independently for each sample. This test is useful in assessing the accuracy of copy number calls, as well as choosing among alternative copy number algorithms or tuning parameter values. Read More

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December 2018

Implementation of a Stirling number estimator enables direct calculation of population genetics tests for large sequence data sets.

Authors:
Swaine L Chen

Bioinformatics 2018 Dec 12. Epub 2018 Dec 12.

Department of Medicine, Division of Infectious Diseases, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; and Infectious Diseases Group, Genome Institute of Singapore, Singapore.

Motivation: Stirling numbers enter into the calculation of several population genetics statistics, including Fu's Fs. However, as alignments become large (>∼50 sequences), the Stirling numbers required rapidly exceed the standard floating point range. Another recursive method for calculating Fu's Fs suffers from floating point underflow issues. Read More

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December 2018

ModL: exploring and restoring regularity when testing for positive selection.

Bioinformatics 2018 Dec 12. Epub 2018 Dec 12.

Department of Mathematics and Statistics, Dalhousie University, Halifax, NS, Canada.

Motivation: Likelihood ratio tests are commonly used to test for positive selection acting on proteins. They are usually applied with thresholds for declaring a protein under positive selection determined from a chi-square or mixture of chi-square distributions. While it is known that such distributions are not strictly justified due to the statistical irregularity of the problem, the hope has been that the resulting tests are conservative and do not lose much power in comparison with the same test using the unknown, correct threshold. Read More

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December 2018

CASMAP: Detection of statistically significant combinations of SNPs in association mapping.

Bioinformatics 2018 Dec 12. Epub 2018 Dec 12.

Department of Biosystems Science and Engineering, ETH Zurich, Basel, 4058, Switzerland SIB Swiss Institute of Bioinformatics.

Summary: Combinatorial association mapping aims to assess the statistical association of higher-order interactions between genetic markers with a phenotype of interest. This paper presents CASMAP, a software package that leverages recent advances in significant pattern mining to overcome the statistical and computational challenges that have hindered combinatorial association mapping. CASMAP can be used to perform region-based association studies and to detect higher-order epistatic interactions of genetic variants. Read More

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December 2018

Commonly misunderstood parameters of NCBI BLAST and important considerations for users.

Bioinformatics 2018 Dec 12. Epub 2018 Dec 12.

Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia.

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December 2018

Gene expression models based on transcription factor binding events confer insight into functional cis-regulatory variants.

Bioinformatics 2018 Dec 12. Epub 2018 Dec 12.

Centre for Molecular Medicine and Therapeutics, Department of Medical Genetics, BC Children's Hospital Research Institute, University of British Columbia, Vancouver, Canada.

Motivation: Deciphering the functional roles of cis-regulatory variants is a critical challenge in genome analysis and interpretation. It has been hypothesized that altered transcription factor (TF) binding events are a central mechanism by which cis-regulatory variants impact gene expression levels. However, we lack a computational framework to understand and quantify such mechanistic contributions. Read More

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December 2018

Agnostic Pathway/Gene Set Analysis of Genome-Wide Association Data Identifies Associations for Pancreatic Cancer.

Authors:
Naomi Walsh Han Zhang Paula L Hyland Qi Yang Evelina Mocci Mingfeng Zhang Erica J Childs Irene Collins Zhaoming Wang Alan A Arslan Laura Beane-Freeman Paige M Bracci Paul Brennan Federico Canzian Eric J Duell Steven Gallinger Graham G Giles Michael Goggins Gary E Goodman Phyllis J Goodman Rayjean J Hung Charles Kooperberg Robert C Kurtz Núria Malats Loic LeMarchand Rachel E Neale Sara H Olson Ghislaine Scelo Xiao O Shu Stephen K Van Den Eeden Kala Visvanathan Emily White Wei Zheng Demetrius Albanes Gabriella Andreotti Ana Babic William R Bamlet Sonja I Berndt Ayelet Borgida Marie-Christine Boutron-Ruault Lauren Brais Paul Brennan Bas Bueno-de-Mesquita Julie Buring Kari G Chaffee Stephen Chanock Sean Cleary Michelle Cotterchio Lenka Foretova Charles Fuchs J Michael M Gaziano Edward Giovannucci Michael Goggins Thilo Hackert Christopher Haiman Patricia Hartge Manal Hasan Kathy J Helzlsouer Joseph Herman Ivana Holcatova Elizabeth A Holly Robert Hoover Rayjean J Hung Vladimir Janout Eric A Klein Robert C Kurtz Daniel Laheru I-Min Lee Lingeng Lu Núria Malats Satu Mannisto Roger L Milne Ann L Oberg Irene Orlow Alpa V Patel Ulrike Peters Miquel Porta Francisco X Real Nathaniel Rothman Howard D Sesso Gianluca Severi Debra Silverman Oliver Strobel Malin Sund Mark D Thornquist Geoffrey S Tobias Jean Wactawski-Wende Nick Wareham Elisabete Weiderpass Nicolas Wentzensen William Wheeler Herbert Yu Anne Zeleniuch-Jacquotte Peter Kraft Donghui Li Eric J Jacobs Gloria M Petersen Brian M Wolpin Harvey A Risch Laufey T Amundadottir Kai Yu Alison P Klein Rachael Z Stolzenberg-Solomon

J Natl Cancer Inst 2018 Dec 12. Epub 2018 Dec 12.

Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD.

Background: Genome-wide association studies (GWAS) identify associations of individual single-nucleotide polymorphisms (SNPs) with cancer risk but usually only explain a fraction of the inherited variability. Pathway analysis of genetic variants is a powerful tool to identify networks of susceptibility genes.

Methods: We conducted a large agnostic pathway-based meta-analysis of GWAS data using the summary-based adaptive rank truncated product method to identify gene sets and pathways associated with pancreatic ductal adenocarcinoma (PDAC) in 9040 cases and 12 496 controls. Read More

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December 2018

CD33 in Alzheimer's Disease - Biology, Pathogenesis, and Therapeutics: A Mini-Review.

Authors:
Lingzhi Zhao

Gerontology 2018 Dec 12:1-9. Epub 2018 Dec 12.

Alzheimer's disease (AD) affects nearly 50 million people worldwide, and currently no disease-modifying treatment is available. With continuous failure of anti-amyloid-beta- or tau-based therapies, identification of new targets has become an urgent necessity for AD prevention and therapy. Recently, conventional genetic approaches and computational strategies have converged on immune-inflammatory pathways as key events in the pathogenesis of AD. Read More

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December 2018
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Single-Cell Transcriptome Profiling of Mouse and hESC-Derived Pancreatic Progenitors.

Stem Cell Reports 2018 Dec;11(6):1551-1564

Diabetes Research Group, BC Children's Hospital Research Institute, Vancouver, BC V5Z 4H4, Canada; Departments of Surgery and Cellular and Physiological Sciences, University of British Columbia, 950 28(th) Avenue West, Vancouver, BC V5Z4H4, Canada. Electronic address:

Human embryonic stem cells (hESCs) are a potential unlimited source of insulin-producing β cells for diabetes treatment. A greater understanding of how β cells form during embryonic development will improve current hESC differentiation protocols. All pancreatic endocrine cells, including β cells, are derived from Neurog3-expressing endocrine progenitors. Read More

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December 2018

Ten-Eleven Translocation Proteins Modulate the Response to Environmental Stress in Mice.

Cell Rep 2018 Dec;25(11):3194-3203.e4

Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA. Electronic address:

5-hydroxymethylcytosine (5hmC) is enriched in brain and has been recognized as an important DNA modification. However, the roles of 5hmC and its writers, ten-eleven translocation (Tet) proteins, in stress-induced response have yet to be elucidated. Here, we show that chronic restraint stress (CRS) induced depression-like behavior in mice and resulted in a 5hmC reduction in prefrontal cortex (PFC). Read More

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December 2018

KLF4, A Gene Regulating Prostate Stem Cell Homeostasis, Is a Barrier to Malignant Progression and Predictor of Good Prognosis in Prostate Cancer.

Cell Rep 2018 Dec;25(11):3006-3020.e7

Department of Cell Biology, NYU School of Medicine, New York, NY 10016, USA; Department of Urology, NYU School of Medicine, New York, NY 10016, USA. Electronic address:

There is a considerable need to identify those individuals with prostate cancer who have indolent disease. We propose that genes that control adult stem cell homeostasis in organs with slow turnover, such as the prostate, control cancer fate. One such gene, KLF4, overexpressed in murine prostate stem cells, regulates their homeostasis, blocks malignant transformation, and controls the self-renewal of tumor-initiating cells. Read More

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December 2018

Corticosteroid use and increased CXCR2 levels on leukocytes are associated with lumacaftor/ivacaftor discontinuation in cystic fibrosis patients homozygous for the F508del CFTR mutation.

PLoS One 2018 12;13(12):e0209026. Epub 2018 Dec 12.

Department of Pediatrics, National Jewish Health, Denver, CO, United States of America.

Cystic fibrosis (CF) is the most common life-shortening genetic disease and is caused by mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene. Several current therapies aim at improving availability and/or function of the mutant CFTR proteins. The combination therapeutic lumacaftor/ivacaftor (Orkambi, luma/iva) partially corrects folding and potentiates CFTR function impaired by the F508del mutation. Read More

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December 2018

Comparison of ground reaction force measurements in a population of Domestic Shorthair and Maine Coon cats.

PLoS One 2018 12;13(12):e0208085. Epub 2018 Dec 12.

Department for Companion Animals and Horses, University Clinic for Small Animals, Small Animal Surgery, Section for Physical Therapy, University of Veterinary Medicine, Veterinärplatz, Vienna, Austria.

Current research on gait analysis mostly involves horses and dogs. Feline kinetics and kinematics are being investigated and receiving more clinical interest at present. Ground reaction forces measured on pressure-sensitive mattresses have been established in healthy Domestic Shorthair cats (DSH). Read More

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December 2018

Genome-wide identification and characterization of gene family for RWP-RK transcription factors in wheat (Triticum aestivum L.).

PLoS One 2018 12;13(12):e0208409. Epub 2018 Dec 12.

Department of Genetics and Plant Breeding, CCS University, Meerut, India.

RWP-RKs represent a small family of transcription factors (TFs) that are unique to plants and function particularly under conditions of nitrogen starvation. These RWP-RKs have been classified in two sub-families, NLPs (NIN-like proteins) and RKDs (RWP-RK domain proteins). NLPs regulate tissue-specific expression of genes involved in nitrogen use efficiency (NUE) and RKDs regulate expression of genes involved in gametogenesis/embryogenesis. Read More

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December 2018

Genome-wide functional analyses of plant coiled-coil NLR-type pathogen receptors reveal essential roles of their N-terminal domain in oligomerization, networking, and immunity.

PLoS Biol 2018 Dec 12;16(12):e2005821. Epub 2018 Dec 12.

Molecular Plant Pathology, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, the Netherlands.

The ability to induce a defense response after pathogen attack is a critical feature of the immune system of any organism. Nucleotide-binding leucine-rich repeat receptors (NLRs) are key players in this process and perceive the occurrence of nonself-activities or foreign molecules. In plants, coevolution with a variety of pests and pathogens has resulted in repertoires of several hundred diverse NLRs in single individuals and many more in populations as a whole. Read More

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December 2018

Social Stress Affects Colonic Inflammation, the Gut Microbiome, and Short Chain Fatty Acid Levels and Receptors.

J Pediatr Gastroenterol Nutr 2018 Dec 11. Epub 2018 Dec 11.

Center for Microbial Pathogenesis, The Research Institute, Nationwide Children's Hospital, Columbus, OH, United States.

Objectives: Gastrointestinal disorders, such as inflammatory bowel diseases (IBD) and functional gastrointestinal disorders (FGID), involve disrupted homeostatic interactions between the microbiota and the host. Both disorders are worsened during stress, and in laboratory mice, stress exposure has been shown to change the composition of the gut microbiome. Stress-induced changes to the microbiome exacerbate intestinal inflammation and alter intestinal motility in mice. Read More

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December 2018

Differential Gene Expression in Erlotinib-treated Fibroblasts.

Nurs Res 2018 Dec 12. Epub 2018 Dec 12.

Assistant Professor, University of South Carolina, College of Nursing, Columbia, SC Bioinformatics Analyst I, University of Maryland, Baltimore, School of Medicine, Institute for Genome Sciences, Baltimore, MD Professor, Chair, Department of Hematology/Oncology, Deputy Director of the Cancer Center for Clinical Research, G. Morris Dorrance Chair in Medical Oncology, Fox Chase Cancer Center, Philadelphia, PA Bioinformatics Analyst II, University of Maryland, School of Medicine, Institute for Genome Sciences, Baltimore, MD Laboratory Research Technician, University of Maryland, Baltimore, School of Nursing, Baltimore, MD Professor, Chair, Department of Pain and Translational Symptom Science, University of Maryland, Baltimore, School of Nursing, Baltimore, MD.

Background: Therapies targeting the epidermal growth factor receptor (EGFR) result in a painful rash, the most common and debilitating toxicity among patients with non-small cell lung cancer (NSCLC) who take EGFR tyrosine kinase inhibitor (TKI) therapy; however, predicting the development and the severity of the rash is difficult.

Objective: To examine how erlotinib-an EGFR TKI that NSCLC patients take to stop or slow tumor growth-altered the transcriptome of dermal fibroblasts.

Methods: Dermal fibroblasts (ATCC® PCS-201-012™) were seeded in cell culture flasks, grown under standard conditions, and transferred to cell culture dishes. Read More

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December 2018

Role of the pre-initiation complex in Mediator recruitment and dynamics.

Elife 2018 Dec 12;7. Epub 2018 Dec 12.

Department of Biomedical Sciences, University at Albany School of Public Health, Albany, United States.

The Mediator complex stimulates the cooperative assembly of a pre-initiation complex (PIC) and recruitment of RNA Polymerase II (Pol II) for gene activation. The core Mediator complex is organized into head, middle, and tail modules, and in budding yeast (), Mediator recruitment has generally been ascribed to sequence-specific activators engaging the tail module triad of Med2-Med3-Med15 at upstream activating sequences (UASs). We show that yeast lacking Med2-Med3-Med15 are viable and that Mediator and PolII are recruited to promoters genome-wide in these cells, albeit at reduced levels. Read More

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December 2018

Structural organization of a major neuronal G protein regulator, the RGS7-Gβ5-R7BP complex.

Elife 2018 Dec 12;7. Epub 2018 Dec 12.

Department of Neuroscience, The Scripps Research Institute, Jupiter, United States.

Signaling by the G protein Coupled Receptors (GPCRs) plays fundamental role in a vast number of essential physiological functions. Precise control of GPCR signaling requires action of Regulators of G protein Signaling (RGS) proteins that deactivate heterotrimeric G proteins. RGS proteins are elaborately regulated and comprise multiple domains and subunits, yet structural organization of these assemblies is poorly understood. Read More

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December 2018

Identification of differentiated functional modules in papillary thyroid carcinoma by analyzing differential networks.

J Cancer Res Ther 2018 Dec;14(Supplement):S969-S974

Department of Ultrasound, Linzi District People's Hospital, Zibo 255 400, Shandong Province, China.

Purpose: The incidence of papillary thyroid carcinoma (PTC) has dramatically increased over the past two decades. This study aimed to investigate the disparity of gene expression between PTC and normal tissues.

Materials And Methods: Gene chip data of E-GEOD-33630 and E-GEOD-60542 were acquired and downloaded from European Bioinformatics Institute Part of the European Molecular Biology Laboratory website. Read More

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December 2018

Proton Countertransport and Coupled Gating in the Sarcoplasmic Reticulum Calcium Pump.

J Mol Biol 2018 Dec 26;430(24):5050-5065. Epub 2018 Oct 26.

Department of Biochemistry and Molecular Biology, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA. Electronic address:

The calcium pump of the sarcoplasmic reticulum (SERCA) is an ATP-driven active transporter of Ca ions that functions via an "alternating-access" cycle mechanism. In each cycle, SERCA transports two Ca ions toward the lumen of the sarcoplasmic reticulum and two to three protons to the cytoplasm. How the latter conformational transition is coupled to cytoplasmic release of protons remains poorly understood. Read More

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December 2018

Quorum quenching: role of nanoparticles as signal jammers in Gram-negative bacteria.

Future Microbiol 2018 Dec 12. Epub 2018 Dec 12.

Department of Microbiology, Government College University, Faisalabad, Pakistan.

Quorum sensing (QS) is a cell density dependent regulatory process that uses signaling molecules to manage the expression of virulence genes and biofilm formation. The study of QS inhibitors has emerged as one of the most fascinating areas of research to discover novel antimicrobial agents. Compounds that block QS have become candidates as unusual antimicrobial agents, as they are leading players in the regulation of virulence of drug-resistant pathogens. Read More

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December 2018
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LncVar: Deciphering Genetic Variations Associated with Long Noncoding Genes.

Methods Mol Biol 2019 ;1870:189-198

CAS Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.

Long noncoding RNAs (lncRNAs) are pervasively transcribed in various species and play important roles in many biological processes. The biological functions of most lncRNAs remain to be explored. Previous studies have revealed that a large amount of disease-associated variations are located in the lncRNA gene regions. Read More

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January 2019

Genome-Wide Annotation of circRNAs and Their Alternative Back-Splicing/Splicing with CIRCexplorer Pipeline.

Methods Mol Biol 2019 ;1870:137-149

CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China.

Circular RNAs (circRNAs) derived from back-spliced exons were sporadically identified about 25 years ago, and have been recently re-discovered genome-wide across different species. Interestingly, one gene locus can generate multiple circRNAs through alternative back-splicing and/or alternative splicing, thus expanding our understanding on the diversity and complexity of transcriptomes. Precise annotation of circRNAs with their alternative back-splicing and alternative splicing events is the basis for the functional characterization of different categories of circRNAs. Read More

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January 2019

HAMR: High-Throughput Annotation of Modified Ribonucleotides.

Methods Mol Biol 2019 ;1870:51-67

Department of Biology, University of Pennsylvania, Philadelphia, PA, USA.

Ribonucleotides can be decorated with over 100 types of covalent chemical modifications. These modifications change the structure, function, and catalytic activity of RNAs, forming a layer of posttranscriptional regulation termed the epitranscriptome. Recent advances in high-throughput mapping have demonstrated these modifications are abundant and mark nearly all classes of RNAs, including messenger RNAs. Read More

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January 2019

Bisulfite Sequencing of RNA for Transcriptome-Wide Detection of 5-Methylcytosine.

Methods Mol Biol 2019 ;1870:1-21

Division of Molecular Biology, Biocenter, Medical University of Innsbruck, Innsbruck, Austria.

A powerful method to determine the methylation status of specific cytosine residues within RNA is bisulfite sequencing. In combination with high-throughput sequencing methods cytosine methylation can be determined at nucleotide resolution on a transcriptome-wide level. Nevertheless, several critical aspects need to be considered before starting such a project. Read More

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January 2019

Identification of Long Noncoding RNA MIR22HG as a Novel Biomarker in Thyroid Cancer.

Pathol Oncol Res 2018 Dec 12. Epub 2018 Dec 12.

Department of Anesthesiology, The First People's Hospital of Jiangxia District Wuhan City, No. 1, Zhifang Culture Avenue, Jiangxia District, Wuhan, Hubei, 430200, People's Republic of China.

Thyroid cancer (TC) is the one of the most common endocrine malignancy. However, currently there are no specific and sensitive biomarkers for predicting the prognosis for TC. In this study, we for the first time showed MIR22HG was down-regulated in thyroid cancer by analyzing public datasets, including TCGA, GSE29265, GSE33630, and GSE55091. Read More

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December 2018

An Overview of DNA Analytical Methods.

Methods Mol Biol 2019 ;1897:385-402

Department of Pathology and Laboratory Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA.

The development of rapid parallel sequencing in the last 20 years has begun a revolution in the field of genetics that is changing nearly all disciplines within biology and medicine. Genomic sequencing has become crucial to the diagnosis and clinical management of patients with constitutional diseases and cancer and has quickly become an integral part of the new era of personalized and precision medicine. The precision medicine initiative, released by the NIH in 2015, has catapulted genomic technologies to the forefront of the practice of medicine and biomedical research. Read More

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January 2019

Nucleic Acid Isolation and Quality Control.

Methods Mol Biol 2019 ;1897:325-343

Technology Center for Genomics and Bioinformatics (TCGB), Department of Pathology and Laboratory Medicine, University of California, Los Angeles, Los Angeles, CA, USA.

This chapter describes the most practical manual and automated methods of isolating genomic DNA and RNA from different sources. It also summarizes currently popular methods of quality control (QC) for genomic DNA, RNA, and next generation sequencing (NGS) libraries. Read More

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January 2019

FOXG1 Regulates PRKAR2B Transcriptionally and Posttranscriptionally via miR200 in the Adult Hippocampus.

Mol Neurobiol 2018 Dec 11. Epub 2018 Dec 11.

Institute of Anatomy and Cell Biology, Department of Molecular Embryology, Faculty of Medicine, Albert-Ludwigs-University Freiburg, 79104, Freiburg, Germany.

Rett syndrome is a complex neurodevelopmental disorder that is mainly caused by mutations in MECP2. However, mutations in FOXG1 cause a less frequent form of atypical Rett syndrome, called FOXG1 syndrome. FOXG1 is a key transcription factor crucial for forebrain development, where it maintains the balance between progenitor proliferation and neuronal differentiation. Read More

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December 2018

T-cell receptor-α CDR3 domain chemical features correlate with survival rates in bladder cancer.

J Cancer Res Clin Oncol 2018 Dec 11. Epub 2018 Dec 11.

Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, USA.

Purpose: In certain cancer settings, a T-cell response to cancer represents a relatively favorable outcome. Thus, the near-future challenges include a better understanding of exactly which T-cell features contribute to a response to which cancer antigen-groups, to maximize the opportunities for tumor-infiltrating lymphocyte (TIL)-based therapies and other immunotherapies.

Methods: The immune receptor complementarity determining region-3 (CDR3) is considered to be important for antigen binding, hence, in this report, we evaluated the chemical features of the CDR3 of 846 T-cell receptor-α (TCR-α) coding regions associated with bladder tumor tissue, using bioinformatics databases. Read More

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December 2018

Differentially expressed serum host proteins in hepatitis B and C viral infections.

Virusdisease 2018 Dec 1;29(4):468-477. Epub 2018 Sep 1.

1Transfusion Transmitted Diseases Department, National Institute of Immunohaematology, 13th floor, New Multi-storeyed Bldg, KEM Hospital Campus, Parel, Mumbai, 400 012 India.

Hepatitis B virus (HBV) and Hepatitis C virus (HCV) infection often lead to hepatocellular carcinoma (HCC), which is mostly detected in advanced stage. Hence, its early detection is of paramount importance using a biomarker having sensitivity and specificity both. The present study highlights differentially expressed host proteins in response to HBV/HCV infection at different stages. Read More

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December 2018

Role of viruses, prions and miRNA in neurodegenerative disorders and dementia.

Virusdisease 2018 Dec 29;29(4):419-433. Epub 2018 Sep 29.

Drug Design & Development Section, Translational Gerontology Branch, Intramural Research Program, National, Institute on Aging, National Institutes of Health, Biomedical Research Center, 251 Bayview Boulevard, Baltimore, MD 21224 USA.

Dementia is known as loss of cellular communications in the brain at a region caused by multi-factorial diseases and pathogenic infections. Approximately eighty percent reported cases of Alzheimer's disease are followed by vascular dementia. The common symptoms of dementia include memory loss, concentration problems, thinking, and language solving situations. Read More

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December 2018

Type I interferon receptor blockade with anifrolumab corrects innate and adaptive immune perturbations of SLE.

Lupus Sci Med 2018 22;5(1):e000286. Epub 2018 Nov 22.

Research Bioinformatics, MedImmune LLC, Gaithersburg, Maryland, USA.

Objective: Anifrolumab is a fully human immunoglobulin G κ monoclonal antibody specific for subunit 1 of the type I interferon (IFN) α receptor. In a phase IIb study of adults with moderate to severe SLE, anifrolumab treatment demonstrated substantial reductions in multiple clinical endpoints. Here, we evaluated serum proteins and immune cells associated with SLE pathogenesis, type I interferon gene signature (IFNGS) test status and disease activity, and how anifrolumab affected these components. Read More

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November 2018

Time Course of Upper Limb Function in Children with Unilateral Cerebral Palsy: A Five-Year Follow-Up Study.

Neural Plast 2018 14;2018:2831342. Epub 2018 Nov 14.

KU Leuven, University of Leuven, Department of Rehabilitation Sciences, Leuven, Belgium.

Knowledge on long-term evolution of upper limb function in children with unilateral cerebral palsy (CP) is scarce. The objective was to report the five-year evolution in upper limb function and identify factors influencing time trends. Eighty-one children (mean age 9 y and 11 mo, SD 3 y and 3 mo) were assessed at baseline with follow-up after 6 months, 1, and 5 years. Read More

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November 2018

Prediction of Drug-Likeness Using Deep Autoencoder Neural Networks.

Front Genet 2018 27;9:585. Epub 2018 Nov 27.

Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China.

Due to diverse reasons, most drug candidates cannot eventually become marketed drugs. Developing reliable computational methods for prediction of drug-likeness of candidate compounds is of vital importance to improve the success rate of drug discovery and development. In this study, we used a fully connected neural networks (FNN) to construct drug-likeness classification models with deep autoencoder to initialize model parameters. Read More

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November 2018

Highlights on the Application of Genomics and Bioinformatics in the Fight Against Infectious Diseases: Challenges and Opportunities in Africa.

Front Genet 2018 27;9:575. Epub 2018 Nov 27.

West African Centre for Cell Biology of Infectious Pathogens, University of Ghana, Accra, Ghana.

Genomics and bioinformatics are increasingly contributing to our understanding of infectious diseases caused by bacterial pathogens such as and parasites such as . This ranges from investigations of disease outbreaks and pathogenesis, host and pathogen genomic variation, and host immune evasion mechanisms to identification of potential diagnostic markers and vaccine targets. High throughput genomics data generated from pathogens and animal models can be combined with host genomics and patients' health records to give advice on treatment options as well as potential drug and vaccine interactions. Read More

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November 2018

Recent Trends in System-Scale Integrative Approaches for Discovering Protective Antigens Against Mycobacterial Pathogens.

Front Genet 2018 27;9:572. Epub 2018 Nov 27.

Department of Biotechnology, Babasaheb Bhimrao Ambedkar University, Lucknow, India.

Mycobacterial infections are one of the deadliest infectious diseases still posing a major health burden worldwide. The battle against these pathogens needs to focus on novel approaches and key interventions. In recent times, availability of genome scale data has revolutionized the fields of computational biology and immunoproteomics. Read More

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November 2018

A Genome-Wide Study of Allele-Specific Expression in Colorectal Cancer.

Front Genet 2018 27;9:570. Epub 2018 Nov 27.

Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China.

Accumulating evidence from small-scale studies has suggested that allele-specific expression (ASE) plays an important role in tumor initiation and progression. However, little is known about genome-wide ASE in tumors. In this study, we conducted a comprehensive analysis of ASE in individuals with colorectal cancer (CRC) on a genome-wide scale. Read More

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November 2018

Generation of 2',3'-Cyclic Phosphate-Containing RNAs as a Hidden Layer of the Transcriptome.

Front Genet 2018 27;9:562. Epub 2018 Nov 27.

Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, United States.

Cellular RNA molecules contain phosphate or hydroxyl ends. A 2',3'-cyclic phosphate (cP) is one of the 3'-terminal forms of RNAs mainly generated from RNA cleavage by ribonucleases. Although transcriptome profiling using RNA-seq has become a ubiquitous tool in biological and medical research, cP-containing RNAs (cP-RNAs) form a hidden transcriptome layer, which is infrequently recognized and characterized, because standard RNA-seq is unable to capture them. Read More

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November 2018

Molecular Epidemiology and Risk Factors of Carbapenemase-Producing Isolates in Portuguese Hospitals: Results From European Survey on Carbapenemase-Producing (EuSCAPE).

Front Microbiol 2018 27;9:2834. Epub 2018 Nov 27.

National Reference Laboratory of Antibiotic Resistances and Healthcare Associated Infections, Department of Infectious Diseases, National Institute of Health Dr. Ricardo Jorge, Lisbon, Portugal.

In Portugal, the epidemiological stage for the spread of carbapenemase-producing (CPE) increased from sporadic isolates or single hospital clones (2010-2013), to hospital outbreaks, later. Here we report data from a 6-month study performed under the European Survey on Carbapenemase-Producing (EuSCAPE). During the study period, 67 isolates (61 and 6 ) non-susceptible to carbapenems were identified in participant hospital laboratories. Read More

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November 2018

Ancestrality and Mosaicism of Giant Viruses Supporting the Definition of the Fourth TRUC of Microbes.

Front Microbiol 2018 27;9:2668. Epub 2018 Nov 27.

Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM); Microbes, Evolution, Phylogeny and Infection (MEΦI); Institut Hospitalo-Universitaire (IHU) - Méditerranée Infection, Marseille, France.

Giant viruses of amoebae were discovered in 2003. Since then, their diversity has greatly expanded. They were suggested to form a fourth branch of life, collectively named 'TRUC' (for "Things Resisting Uncompleted Classifications") alongside , , and . Read More

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November 2018

Integrated analysis reveals key genes with prognostic value in lung adenocarcinoma.

Cancer Manag Res 2018 21;10:6097-6108. Epub 2018 Nov 21.

Department of Respiratory Medicine, The Affiliated Huaian No. 1 People's Hospital of Nanjing Medical University, Huai'an, Jiangsu, People's Republic of China,

Background: Lung cancer is one of the most common malignant tumors. Despite advances in lung cancer therapies, prognosis of non-small-cell lung cancer is still unfavorable. The aim of this study was to identify the prognostic value of key genes in lung tumorigenesis. Read More

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November 2018

TRIM2 downregulation in clear cell renal cell carcinoma affects cell proliferation, migration, and invasion and predicts poor patients' survival.

Cancer Manag Res 2018 20;10:5951-5964. Epub 2018 Nov 20.

Department of Urology, The First Affiliated Hospital of Xiamen University, Xiamen 361003, China,

Background And Aim: Tripartite motif containing (TRIM) family protein has been involved in multiple pathogenesis of cancers. TRIM2 is a member of the family, and its role in clear cell renal cell carcinoma (ccRCC) remains to be unclarifid. Here, we showed the clinical value and biological role of TRIM2 in ccRCC. Read More

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November 2018

Epidemiological characteristics and genetic structure of linezolid-resistant .

Infect Drug Resist 2018 20;11:2397-2409. Epub 2018 Nov 20.

State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China,

Objectives: The aim of this study was to investigate the mechanism of linezolid resistance and evaluate the risk factors for linezolid-resistant (LZR-Efa) infections.

Methods: A total of 730 isolates were collected, and whole-genome sequencing and bioinformatics analysis were performed. Meanwhile, risk factors related to linezolid resistance were analyzed by binary logistic regression. Read More

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November 2018
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Aberrantly expressed long noncoding RNAs and genes in Parkinson's disease.

Neuropsychiatr Dis Treat 2018 22;14:3219-3229. Epub 2018 Nov 22.

Department of Neurology, The Second Affiliated Hospital of Nantong University, The First People's Hospital of Nantong, Nantong, China,

Purpose: Parkinson's disease (PD) is a common neurodegenerative movement disorder, but the pathogenesis remains elusive. This study was aimed to explore key genes and long noncoding RNAs (lncRNAs) associated with PD.

Materials And Methods: Three patients with PD and three normal controls were enrolled in the present study from July 12, 2017, to August 29, 2017. Read More

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November 2018

Histone demethylase LSD1 is required for germinal center formation and BCL6-driven lymphomagenesis.

Nat Immunol 2019 Jan 10;20(1):86-96. Epub 2018 Dec 10.

Department of Medicine, Division of Hematology & Medical Oncology, Weill Cornell Medicine, New York, NY, USA.

Germinal center (GC) B cells feature repression of many gene enhancers to establish their characteristic transcriptome. Here we show that conditional deletion of Lsd1 in GCs significantly impaired GC formation, associated with failure to repress immune synapse genes linked to GC exit, which are also direct targets of the transcriptional repressor BCL6. We found that BCL6 directly binds LSD1 and recruits it primarily to intergenic and intronic enhancers. Read More

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January 2019